Version 1.0.6: Hotkeys (shortcuts to capture screenshots) are now configurable. Compatibility fix for Win 8, Win 2008 servers and 64 bit machines. Jul 13, 2011 Version 1.0.6: Hotkeys (shortcuts to capture screenshots) are now configurable. Compatibility fix for Win 8, Win 2008 servers and 64 bit machines. Overall Hive 3.1.2 on MR3 0.10 runs slightly slower than Hive-LLAP and Hive 4.0.0-SNAPSHOT on MR3 0.10. For long-running queries such as query 16, 23, 24, 67, and 95, large discrepancies in the running time are due to different query plans (i.e., results of compiling queries), not differences in the performance of the underlying systems. The threshold for PCIe 3.0 x8 in this title appears to be just over 300 fps, while x16 will allow for almost 360 fps and PCIe 4.0 x16 doesn’t limit the 3950X, allowing for 368 fps on average.
Overview:
The primary goal of MetaMapLite to provide a near real-time named-entity recognizer which is not a rigorous as MetaMap but is much faster while allowing users to customize and augment its behavior for specific purposes. MetaMapLite uses some of the tables originally developed for MetaMap. Currenty, MetaMapLite does not support dynamic variant generation. Named Entities are found using longest match. Restriction by UMLS source and Semantic type is optional. Part-of-speech tagging which improves precision by a small amount (at the cost of speed) is also optional. Negation detection is available using either Wendy Chapman's context or a native negation detection algorithm based on Wendy Chapman's NegEx which is somewhat less effective, but faster.
You can use MetaMap on the web at the Interactive MetaMapLite Page. (A ReSTful service provided by the server is described on the 'MetaMapLite ReSTful client page'.
Prerequisites:
- MetaMapLite requires a minimum of 16GB of disk space when it has been uncompressed.
- MetaMapLite requires a minimum of 2GB of memory to run. At least 4GB is recommended.
- You will need a working version of bunzip2 or WinZip or 7-Zip to uncompress the MetaMapLite download file depending on which one you download. If you do not have a copy of bunzip2, it is available from http://www.bzip.org/. Similarly, WinZip is available from http://www.winzip.com/. And 7-Zip is available at http://www.7-zip.org.
- To run MetaMapLite, you will need the Java Runtime Environment (JRE). We have tested MetaMapLite with JRE 1.8. The JRE is available from: http://www.java.com
- To use MetaMapLite, you must comply with the MetaMap Terms and Conditions.
- To download MetaMapLite, you must have accepted the terms of the UMLS Metathesaurus License Agreement, which requires you to respect the copyrights of the constituent vocabularies and to file a brief annual report on your use of the UMLS. You also must have activated a UMLS Terminology Services (UTS) account. For information on how we use UTS authentication please select the Info icon to the right:
For details of the licenses see the UMLS Metathesaurus License Agreement and How to License and Access the Unified Medical Language System® (UMLS®) Data.
Downloads
MetaMapLite 3.6.2rc6 and 2020
- MetaMapLite 3.6.2rc6 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- 2020AB UMLS Level 0+4+9 Dataset(WinZip - 1g), [sha1sum], [md5sum]
- 2020AA UMLS Level 0+4+9 Dataset(WinZip - 1g), [sha1sum], [md5sum]Note: users who have downloaded the 2020AA USAbase data set distribution before May 15th: The 2020AA USAbase data set that was published on this website was missing the SNOMEDCT_US vocabulary. The affected archives have the following checksums: The archives have been replaced with ones containing the SNOMEDCT_US vocabulary.
- 2020AA UMLS Level 0 Dataset(WinZip - 877m), [sha1sum], [md5sum]
![Isnapshot 3 4 0 Isnapshot 3 4 0](https://image.slidesharecdn.com/presentation1-120301083000-phpapp01/95/what-does-isnapshot-do-1-638.jpg?cb=1422559724)
MetaMapLite 3.6.2rc5 and 2020AA datasets
- MetaMapLite 3.6.2rc5 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- 2020AA UMLS Level 0+4+9 Dataset(WinZip - 1g), [sha1sum], [md5sum]Note: users who have downloaded the 2020AA USAbase data set distribution before May 15th: The 2020AA USAbase data set that was published on this website was missing the SNOMEDCT_US vocabulary. The affected archives have the following checksums: The archives have been replaced with ones containing the SNOMEDCT_US vocabulary.
- 2020AA UMLS Level 0 Dataset(WinZip - 877m), [sha1sum], [md5sum]
3/4 Inch To Mm
) in the same directory: Change to the 'public_mm_lite' directory and use the '--indexdir' option to specify the location of the dataset(shown using a relative path): The path for the level 0+4+9 dataset is data/ivf/2020AA/USAbase.MetaMapLite 3.6.2rc3 and 2018AB datasets
- MetaMapLite 2018 3.6.2rc3 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- 2018AB UMLS Level 0 Dataset(WinZip - 721m), [sha1sum], [md5sum]
- 2018AB UMLS Level 0+4+9 Dataset(WinZip - 1g), [sha1sum], [md5sum]
I-snapshot 3 4 0 Download
To use extract the archive public_mm_lite_3.6.2rc3_binaryonly.zip and dataset archive (public_mm_data_lite_base_2018ab_ascii.zip or public_mm_data_lite_usabase_2018ab_ascii.zip) in the same directory: Change to the 'public_mm_lite' directory and use the '--indexdir' option to specify the location of the dataset(shown using a relative path): The path for the level 0+4+9 dataset is data/ivf/2018ABascii/USAbase.MetaMapLite 3.6.2rc3
The 3.6.2rc2 version of MetaMapLite is a release candidate for version 3.6.2
- Fixed error in tokenization when calling OpenNLP's Part-of-Speech tagger
- Merged UTF-8 handling code from UTF branch into master
- MetaMapLite 2018 3.6.2rc3 with Category 0 (Base) 2018AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc3 with Category 0+4+9 (USAbase) 2018AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc3 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc3 USABase (Category 0+4+9) data Version(WinZip - 1.2GB), [sha1sum], [md5sum]
MetaMapLite 3.6.2rc2
The 3.6.2rc2 version of MetaMapLite is a release candidate for version 3.6.2 that fixes the following issues:
- When using EntityLookup4 (i.e., setting metamaplite.enable.scoring = false), disabling postagging (i.e., setting metamaplite.enable.postagging = false) significantly reduces the number of entities found. On the same collection, I go from a median of 50 entities per document (with postagging = true) to a median of 0 entities per document (with postagging = false).
- When using MetaMapLite, EntityLookup4 is initialized every time processDocumentList list is called and again each time processDocument is called, while EntityLookUp5 is only re-initialized when needed.
- When using a non-standard data directory, the property: opennlp.en-pos.bin.path: $DATA_DIR/ models/en-pos-maxent.bin must be set. This property is not supplied in the template config file and MML falls back to using the hardcoded default value which results in a crash. It may be helpful to add this property to the generated config file so if a user is customizing their data directory they will know to adjust the properties accordingly.
- When using a non-standard data directory, the following properties must be set for MMI file output or null pointer exceptions are thrown:
- metamaplite.index.directory: $DATA_DIR/ivf/2017AA/Base/strict/indices/
- metamaplite.ivf.meshtcrelaxedindex: $DATA_DIR/ivf/2017AA/Base/strict/indices/meshtcrelaxed
- MetaMapLite 2018 3.6.2rc2 with Category 0 (Base) 2018AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc2 with Category 0+4+9 (USAbase) 2018AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc2 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc2 USABase (Category 0+4+9) data Version(WinZip - 1.2GB), [sha1sum], [md5sum]
MetaMapLite 3.6.1p1
The 3.6.1p1 version of MetaMapLite is a bugfix release that fixes the following issue:
- Fixes an error where docid is not propagated to Entity records in output result.
- MetaMapLite 2017 3.6.1p1 with Category 0 (Base) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6.1p1 with Category 0+4+9 (USAbase) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6.1p1 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6.1p1 USABase (Category 0+4+9) data Version(WinZip - 1.2GB), [sha1sum], [md5sum]
MetaMapLite 3.6.1
The 3.6.1 version of MetaMapLite is a bugfix release that fixes the following issue:
- Fixes an error in the method which removes entities which are subsumed by a larger entity in which some entities that were not subsumed were removed.
- MetaMapLite 2017 3.6.1 with Category 0 (Base) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6.1 with Category 0+4+9 (USAbase) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6.1 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6.1 USABase (Category 0+4+9) data Version(WinZip - 1.2GB), [sha1sum], [md5sum]
MetaMapLite 3.6
The 3.6 version of MetaMapLite is a bugfix release that fixes the following issues:
- Fixes an error in the longest match algorithm in which entities which were subsumed by a longer enitity were not removed.
- Includes an example of creating a result formatter.
- Readme documentation has been updated.
- MetaMapLite 2017 3.6 with Category 0 (Base) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6 with Category 0+4+9 (USAbase) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2017 3.6 USABase (Category 0+4+9) data Version(WinZip - 1.2GB), [sha1sum], [md5sum]
MetaMapLite 3.5
The 3.5 version of MetaMapLite is a bugfix release that fixes the following issues:
- The negation status of a concept was not refected in the MMI fielded output.
- The location of chunker model file was not user modifiable.
- The default properties file was missing a reference to the treecodes file used for MMI fielded output.
- Readme documentation has been updated.
- MetaMapLite 2017 3.5 with Category 0 (Base) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.5 with Category 0+4+9 (USAbase) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.5 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
MetaMapLite 3.4
The 3.4 version of MetaMapLite now optionally adds scoring similar to the original MetaMap of concept mapping results for BRAT output and ranked indexing results for MMI Output using MetaMap's Ranked Indexing algorithm. MMI Results may be somewhat different from MetaMap's due to differences in MetaMapLite's mapping scores which are supplied as input to the MMI Ranked Indexing algorithm.
- MetaMapLite 2017 3.4 with Category 0 (Base) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2017 3.4 with Category 0+4+9 (USAbase) 2017AA UMLS dataset(WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2016 3.1 SNAPSHOT
- MetaMapLite 2016 3.1 SNAPSHOT Version(WinZip - 601 MB), [sha1sum], [md5sum]
- MetaMapLite 2016 3.1 SNAPSHOT Version(Bzip2 Tar - 544 MB), [sha1sum], [md5sum]
MetaMapLite 2016 3.0 SNAPSHOT
- MetaMapLite 2016 3.0 SNAPSHOT Version(Bzip2 Tar - 544 MB), [sha1sum], [md5sum]
Example MetaMapLite Servlet
- Example of using MetaMapLite in a Servlet instance. The archive provides a minimal example of ANT project demonstrating the use of MetaMapLite in a servlet instance.
Documentation
MetaMapLite README Documentation
- MetaMapLite 3.0 README Documentation(Last Updated: September 26, 2016)
MetaMapLite Source Code
Publications
MetaMap Lite: an evaluation of a new Java implementation of MetaMap. Demner-Fushman D., Rogers WJ, Aronson AR. JAMIA. Volume 24, Issue 4, July 2017.DOI: 10.1093/jamia/ocw177. URL: https://academic.oup.com/jamia/issue/24/4. ALT URL: https://www.ncbi.nlm.nih.gov/pubmed/28130331.Sources
The Source code for MetaMapLite is supplied with the distribution in the directorypublic_mm_lite/src
. The source code is also available at the MetaMapLite Github Page.